Genetic consequences of using seed mixtures in restoration: A case study of a wetland plant Lychnis flos-cuculi

Sowing with seed mixtures is a common practice in restoring species-rich communities in areas with impoverished species pools. The potential genetic consequences of using these mixtures, however, are poorly understood and often not considered in practical restoration. We investigated genetic diversity, inbreeding and genetic structure of samples collected from 26 populations of the common wetland plant species Lychnis flos-cuculi in an agricultural region in Switzerland. Some of these populations were natural, while others had been sown several years ago. This enabled us to compare the genetic composition of populations of indigenous origin with those originating from commercially produced seed mixtures. Gene diversity and allelic richness were similar in natural and sown populations. In contrast, inbreeding coefficients were three times higher in sown than in natural populations. The sown populations were genetically distinct from the native populations. We distinguished two homogeneous gene pools that presumably originated from different source populations used to produce seed mixtures. The use of commercially produced seeds may alter the genetic diversity and structure of plant populations. The observed higher inbreeding coefficients of sown populations could lead to reduced population viability. To restore genetically diverse populations, the seeds for further propagation should be collected from numerous individuals in large and non-isolated populations nearby restored sites. Ex situ stocks for the production of commercial seed mixtures should only be propagated for a few generations to avoid negative effects such as inbreeding or loss of local adaptation.     

Diversity of 21 taro (Colocasia esculenta (L.) Schott) accessions of Andaman Islands

The genetic diversity of taro (Colocasia esculenta (L.) Schott.) accessions growing naturally in Andaman Islands was analysed using morphological and DNA markers. Twenty one representative samples of C. esculenta from different parts of Islands in addition to three commercial varieties as reference genotypes were used in study. About 63% phenotypic variation was observed in C. esculenta A total number of 491 amplified fragments were obtained of which 347 showed polymorphic banding patterns. The accessions were grouped into two major clusters with both RAPD and ISSR markers with 56 and 57% diversity, respectively. The reference genotypes were grouped into one group and island population in other cluster. Both marker systems divided population into two sub clusters and showed correlation with morphological parameters. The diversity pattern observed in present study showed rich genetic diversity of C. esculenta in Andaman Islands provided simple strategy for reducing repeatability of taro germplasm in gene banks. The study also suggested pre-evaluation of germplasm using molecular and morphological markers to enhance efficiency of exploration trips.     

Genetic consequences of animal translocations: A case study using the field cricket, Gryllus campestris L.

Animal relocations have become a common tool in nature conservation, but the genetic consequences of such projects have rarely been studied in insects. As both natural and artificial formation of new populations may lead to genetic drift (founder effect), decreased genetic diversity and increased rates of inbreeding, genetic analyses can provide valuable information to evaluate the success of a relocation project. The field cricket (Gryllus campestris) has been subjected to reintroduction and translocation projects in England and northern Germany. Here, we present a microsatellite study on the population genetics of one recently established population of this species in comparison with several older populations and some recently colonized sites. Our results show that the translocation did not result in a significant loss of genetic diversity, when compared to source and other natural populations suggesting that translocation of a high number of nymphs from different subpopulations may be a suitable method to decrease the loss of genetic diversity and reduce the risk of inbreeding. Furthermore, the translocation had no negative effect on the source population, which reached a new maximum population size in 2006. An assignment test showed that individuals from the translocated population (F4 generation) were still assigned to the source populations, whereas two young subpopulations that originated by natural colonization from the central population about ten years ago already formed separate genetic clusters. As the strong fragmentation of G. campestris populations in northern Germany hampers natural colonization of newly created potential habitats, translocation projects seem to be an appropriate method to preserve this species.     

Genetic diversity in wild and cultivated black raspberry (Rubus occidentalis L.) evaluated by simple sequence repeat markers

Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars have been noted for showing very few phenotypic differences and seedlings from crosses between cultivars for a lack of segregation for important traits. Despite these challenges, little molecular work has been done to explore genetic diversity and relationships in wild and cultivated black raspberry germplasm. Microsatellite, or simple sequence repeat (SSR), markers are highly polymorphic codominant markers useful for studying genetic diversity, population genetics, genetic fingerprinting and other applications. We examined genetic diversity in 148 wild and cultivated black raspberry accessions using 21 polymorphic SSR markers. Black raspberry cultivars clustered tightly and showed higher than expected heterozygosity while that of wild accessions was low. Relationships between wild black raspberry accessions were poorly resolved and regional clusters were mostly absent from our analysis. Our results indicated that wild black raspberry germplasm is a relatively untapped resource available for future breeding.     

三个野生种群马氏珠母贝遗传多样性的RAPD分析

摘要：为了解野生种群马氏珠母贝（Pimctada martensii (Dunker.)）的遗传结构背景和开展遗传改良育种,运用RAPD技术分析了海南三亚（SW）、广东大亚湾（DW）和广西北海（BW）3个野生种群的遗传多样性。采用了18个10碱基的随机引物对3个野生种群进行分析,其中6个引物能扩增出清晰的多态带谱,扩增的DNA片段大小在含0.2~3.0 kb之间。SW、DW和BW 3个种群内的遗传相似性指数分别为0.642、0.672和0.688,Shannon多样性值分别为0.266、0.211和0.174。马氏珠母贝3个野生种群的遗传相似性依次为SW< DW < BW,而遗传多样性依次是SW > DW> BW。DW和SW相对遗传距离为0.104;DW和BW相对遗传距离为0.094;SW和BW相对遗传距离为0.212。讨论了马氏珠母贝野生种群遗传多样性差异的可能原因、种群间杂交子代的杂交优势预测及人工养殖对野生种群遗传结构的可能影响。     

Temporal genetic analysis of the critically endangered oriental white-backed vulture in Pakistan

Populations of oriental white-backed vultures (Gyps bengalensis) in south Asia have declined over 95% since the mid-1990s due to feeding on livestock carcasses that had been treated with diclofenac, an anti-inflammatory pharmaceutical that is fatal to Gyps vultures. To prevent extinction, captive breeding efforts have been initiated; however, given the overall decline, it is not known to what extent levels of genetic diversity currently exist in the remaining populations. Here we document temporal genetic diversity levels during the 2000-2006 interval for the last remaining breeding colony of oriental white-backed vultures in Pakistan, and show with simulations that a much larger captive population size is required than currently maintained to prevent further loss of genetic diversity. Before this species is extinct in the wild, it is crucial that additional individuals are included in the captive population.     

Population viability analysis of European bison populations in Polish and Belarusian parts of Bia?owie?a Forest with and without gene exchange

European bison (Bison bonasus) became extinct in the wild at the beginning of the 20th century. The contemporary Lowland line of bison was founded by seven individuals that survived in captivity. The largest population of Lowland bison live in the Bia?owie?a Forest, but the forest and the population are divided by a border fence between Poland and Belarus. This fence is a barrier to the movement of ungulates. In this study, we used population genetic models to predict the future viability of the Polish and Belarusian bison populations. We determined the founder contribution, founder equivalent, mean inbreeding coefficient, mean kinship, and the proportion of genetic diversity retained in the Belarusian bison population. Although the founding group of the Belarusian population was larger than that of the Polish population, the latter had more favourable genetic parameters. We assessed inbreeding depression for fecundity in free-ranging European bison compared to captive individuals. Using population viability analysis (PVA) we modelled both bison populations with or without gene exchange, and with or without incorporating the kinship of the founders. When founder kinship was included, in both populations the mean number of alleles and the gene diversity retained within extant populations decreased substantially compared to PVA models in which founders were not related. The worst genetic parameters were obtained for the Belarusian population under a scenario in which the founders are related and gene exchange is lacking, which is the closest to the real situation. Creation of passages for animals by partial removal of the border fence would have a favourable effect on the genetic variation and viability of both bison populations, especially the Belarusian.     

Cryptic genetic bottlenecks during restoration of an endangered tropical conifer

Forest restoration programmes aim to use material for re-planting that is genetically diverse and not inbred. However, restricted seed sampling, high variance in reproductive output, and the production of inbred seeds that survive in the nursery but not in the wild can lead to forest restoration stock being genetically compromised. The aim of this study was to evaluate whether the reproductive biology of the New Caledonian endemic conifer Araucaria nemorosa makes it susceptible to these genetic problems and to assess whether there is evidence for genetic bottlenecks and elevated inbreeding in nursery stock compared to seedlings and adults from wild source populations. Reproductive output was low with high variance among trees (only 14% of adult trees surveyed produced mature cones, >50% of examined cones had <10 viable seeds). Evidence for an extreme genetic bottleneck was detected in a nursery population established from cones collected from adult trees. A second nursery population established with seed collected from the forest floor showed no evidence of a genetic bottleneck, but was inbred compared to its wild source population. In light of these results, we do not recommend collecting cones directly from A. nemorosa as an efficient means of establishing genetically diverse stock for restoration programmes. Collecting seed from the forest floor is likely to be more effective, but the planting stock may contain a high proportion of inbred individuals. Collecting established wild seedlings already subjected to natural selection is suggested as an alternative method of maximising the diversity captured, whilst minimising sampling effort and proportion of inbred individuals.     

Rare species

An operational definition of rare species might include the specification that it either occurs in widely separated, small sub-populations so that interbreeding between sub-populations is seriously reduced, or is restricted to a single population. It has usually been assumed that depauperization of habitat and reduction of genetic material have occurred in rare species, but recent studies of electrophoretically identified genetic polymorphisms suggest that some small populations and some inbreeding populations may retain considerable heterogeneity. Because different populations of a species tend to differ in genetic composition, one would expect the number of sub-populations to be more important for the population's security than the total population size. Specialization of an isolated inbreeding population to a restricted homogeneous habitat under pressure of competition should have serious ecological consequences. This reasoning suggests several conclusions. The protection of an isolated, reduced population in its present state may encourage further specialization and conservatism. In rehabilitating a relict population a first step might be to encourage it to break up into largely, but not completely, independent sub-populations. In a breeding programme, variability should be deliberately promoted as well as quick turnover between the breeding population and the wild. Very high mortality of released individuals must be expected, because it is the rule in the wild even in a rapidly increasing population.     

Population management of threatened taxa in captivity within their natural ranges: Lessons from Andean bears (Tremarctos ornatus) in Venezuela

Populations of threatened taxa in captivity within their natural ranges can make important contributions to conservation, but these may be compromised by the inappropriate application of population management goals developed in other contexts. We conducted demographic, genetic, and population viability analyses on the captive population of Andean bears (Tremarctos ornatus) in Venezuela to investigate the management of within-range captive populations in general, and to better integrate this population into the conservation of Andean bears in particular. We found that although the present population is very small and not internally self-sustaining, incorporation of confiscated wild individuals has resulted in a low average number of generations in captivity and low inbreeding, with moderate gene diversity and a high probability of future population persistence. However, past imports from extra-range populations have been from over-represented lineages of unknown origin, which have mixed with under-represented Venezuelan ones, reducing the future value of the Venezuelan population as a source for founder stock. Our analyses indicate that the rate of incorporation of wild recruits is a major factor influencing proxy measures of conservation value, and distinguishing within- from extra-range populations. This implies that, contrary to conventional wisdom, internal self-sustainability can be a misguided goal in within-range populations, which furthermore may not be suitable destinations for surplus animals from captive populations elsewhere.     

Genetics and extinction

The role of genetic factors in extinction has been a controversial issue, especially since Lande’s paper [Genetics and demography in biological conservation, Science 241 (1988) 1455-1460] paper in Science. Here I review the evidence on the contribution of genetic factors to extinction risk. Inbreeding depression, loss of genetic diversity and mutation accumulation have been hypothesised to increase extinction risk. There is now compelling evidence that inbreeding depression and loss of genetic diversity increase extinction risk in laboratory populations of naturally outbreeding species. There is now clear evidence for inbreeding depression in wild species of naturally outbreeding species and strong grounds from individual case studies and from computer projections for believing that this contributes to extinction risk. Further, most species are not driven to extinction before genetic factors have time to impact. The contributions of mutation accumulation to extinction risk in threatened taxa appear to be small and to require very many generations. Thus, there is now sufficient evidence to regard the controversies regarding the contribution of genetic factors to extinction risk as resolved. If genetic factors are ignored, extinction risk will be underestimated and inappropriate recovery strategies may be used.     

Capturing genetic diversity of wild populations for <Emphasis Type="Italic">ex situ</Emphasis> conservation: Texas wild rice (<Emphasis Type="Italic">Zizania texana</Emphasis>) as a model

Genebanks complement other conservation programs because they preserve genetic diversity needed for future breeding and restoration. We evaluated efficiency of capturing genetic diversity, using endangered Zizania texana (Texas wild rice) as a model for plants with recalcitrant seeds. This perennial aquatic grass is restricted to 4 km of the San Marcos River in Texas. An early conservation collection included plants from stands throughout the river, based on the assumption stands would be unique genotypes. Using microsatellite markers, we found that genetic diversity was concentrated in five of 15 large, demographically stable stands; 96 stands smaller than 2 m² contributed no unique alleles. High heterozygosity and few duplicate genotypes suggested that sexual reproduction occurs more often than presumed. Simulations of stratified sampling of large stands captured all alleles in only 45 individuals, while random sampling along the river captured much less diversity. The early conservation collection captured as much diversity as expected from random sampling. Texas wild rice stands resemble a mainland-island metapopulation; our analyses suggest that stratified sampling maximizes genetic diversity for this population dynamic. Demographic and genetic information is important for validating the design of efficient ex situ collections and guiding in situ conservation.     

Adapting clonally propagated crops to climatic changes: a global approach for taro (<Emphasis Type="Italic">Colocasia esculenta</Emphasis> (L.) Schott)

Clonally propagated crop species are less adaptable to environmental changes than those propagating sexually. DNA studies have shown that in all countries where taro (Colocasia esculenta (L.) Schott) has been introduced clonally its genetic base is narrow. As genetic variation is the most important source of adaptive potential, it appears interesting to attempt to increase genetic and phenotypic diversity to strengthen smallholders’ capacity to adapt to climatic changes. A global experiment, involving 14 countries from America, Africa, Asia and the Pacific was conducted to test this approach. Every country received a set of 50 indexed genotypes in vitro assembling significant genetic diversity. After on-station agronomic evaluation trials, the best genotypes were distributed to farmers for participatory on-farm evaluation. Results indicated that hybrids tolerant to taro leaf blight (TLB, Phytophthora colocasiae Raciborski), developed by Hawaii, Papua New Guinea and Samoa breeding programmes outperformed local cultivars in most locations. However, several elite cultivars from SE Asia, also tolerant to TLB, outperformed improved hybrids in four countries and in one country none of the introductions performed better than the local cultivars. Introduced genotypes were successfully crossed (controlled crossing) with local cultivars and new hybrids were produced. For the first time in the history of Aroids research, seeds were exchanged internationally injecting tremendous allelic diversity in different countries. If climatic changes are going to cause the problems envisaged, then breeding crops with wide genetic diversity appears to be an appropriate approach to overcome the disasters that will otherwise ensue.     

Genetic diversity and gene flow dynamics revealed in the rare mixed populations of wild soybean (Glycine soja) and semi-wild type (Glycine gracilis) in China

Thus far, there is little knowledge of the genetic diversity, structure and gene flow dynamics in rare wild and semi-wild soybean mixed populations, and such information is vital for understanding of the origin of semi-wild soybean (Glycine gracilis) and the biosafety protection of wild soybean from transgenic soybeans. Population eco-genetic data are necessary to provide a more coherent and comprehensive understanding of the genetic events that occurred in the natural habitats of wild soybean (Glycine soja). We tested genetic diversity and structure of 11 wild mixed populations of wild soybean (Glycine soja) and semi-wild soybean (G. gracilis), 1 wild soybean population, and 1 cultivated soybean variety population were studied using 20 nuclear microsatellite markers (SSRs). We found based on microsatellite polymorphisms that the mixed populations were characterized by higher mean heterozygosity (H _o = 0.029) and outcrossing rate (t _m = 6.35 %), and lower fixation index (F _is = 0.891), and the semi-wild plants had distinctly higher heterozygosity (H _o = 0.081) than that of the wild plants (H _o = 0.007). The occurrence of semi-wild plants influenced population genetic structure but not geographical population differentiation. These mixed populations exhibited strong ecogeographical differentiation, which suggests that their original populations were colonized over a long phytogeographical history. The introgression occurred through pollen gene flow from the soybean fields into wild populations and created the semi-wild plants, with significant genetic differentiation from the typical wild ones. Introgressive genes could become established by two possible modes in wild soybean populations by both self-segregation and/or intrapopulation secondary hybridization. The latter deserves attention because of the possibility of rapid transgene escape.     

A cooperative breeding programme for the Mongolian wild horse Equus przewalskii in the United States

The Mongolian wild horse Equus przewalskii (Poliakov, 1881) has been propagated in captivity for ten generations. Well over a decade has passed since the last confirmed sightings of E. przewalskii in its historic range. Concern over the extent of inbreeding which has occurred during the captive propagation of this endangered species has led to numerous recommendations for management of captive stock as genetic populations rather than isolated collections. In November 1979 a meeting was held of North American Przewalski's horse breeders, at which time a coordinated breeding programme was considered and adopted by all institutions breeding E. przewalskii in the United States. As a result of this agreement, a number of animal movements between zoos have occurred with a projected decrease in the extent of inbreeding of foals of the next generation. The history of propagation of E. przewalskii in the United States and the genetic considerations involved in the management programme are discussed.     

Polygyny and female breeding failure reduce effective population size in the lekking Gunnison sage-grouse

Populations with small effective sizes are at risk for inbreeding depression and loss of adaptive potential. Variance in reproductive success is one of several factors reducing effective population size (N_e) below the actual population size (N). Here, we investigate the effects of polygynous (skewed) mating and variation in female breeding success on the effective size of a small population of the Gunnison sage-grouse (Centrocercus minimus), a ground nesting bird with a lek mating system. During a two-year field study, we recorded attendance of marked birds at leks, male mating success, the reproductive success of radio-tagged females, and annual survival. We developed simulations to estimate the distribution of male reproductive success. Using these data, we estimated population size () and effective population size N_e for the study population. We also simulated the effects of population size, skewed vs. random mating, and female breeding failure on N_e. In our study population, the standardized variance in seasonal reproductive success was almost as high in females as in males, primarily due to a high rate of nest failure (73%). Estimated N_e (42) was 19% of in our population, below the level at which inbreeding depression is observed in captive breeding studies. A high hatching failure rate (28%) was also consistent with ongoing inbreeding depression. In the simulations, N_e was reduced by skewed male mating success, especially at larger population sizes, and by female breeding failure. Extrapolation of our results suggests that six of the seven extant populations of this species may have effective sizes low enough to induce inbreeding depression and hence that translocations may be needed to supplement genetic diversity.     

Analysis of genetic diversity in Indian taro [Colocasia esculenta (L.) Schott] using random amplified polymorphic DNA (RAPD) markers

Taro [Colocasia esculenta (L.) Schott] germplasm accessions collected from different parts of India were subjected to RAPD (Random Amplified Polymorphic DNA) analysis to assess the genetic diversity prevalent and also to test the genetic basis of morphotypic classification. Thirteen random decamer primers out of the 22 tested were used to analyse 32 taro accessions belonging to 28 morphotypes. Three out of these thirteen primers analysed showed 100 per cent polymorphism. Per cent polymorphism varied from 60 to 100 among the polymorphic primers. High genetic diversity was revealed as the similarity coefficient values ranged from 0.50 to 0.98. No two accessions analysed in the present study showed a similarity coefficient value of one thereby indicating their distinctness and presence of high genetic diversity in Indian taro germplasm. Dendrogram obtained from UPGMA analysis grouped 32 accessions in four clusters and three accessions were placed as outliers. Clustering pattern did not show any strict relationship with geographical distribution, morphotype classification and genotypic diversity. Further, accessions classified, as belonging to the same morphotypic group did not always cluster together. Presence of a very close genepool of the wild, weedy and cultivated forms with extreme levels of phenotypic and genotypic variation is suggested as the reason for high genetic diversity reported. Usefulness of DNA markers such as RAPD in characterising and assessing the genetic diversity in Indian taro germplasm is hereby demonstrated.     

Genetic diversity and local population structure of fragmented populations of Trillium camschatcense (Trilliaceae)

Trillium camschatcense, a long-lived common woodland herb, has been experiencing intensive habitat fragmentation over the last century in eastern Hokkaido, Japan. We examined the genetic diversity and population genetic structure of 12 fragmented populations with different population sizes using allozyme electrophoresis. The percentage of polymorphic loci and mean number of alleles per locus were positively related to population size, probably due to the stochastic loss of rare alleles (frequency of q<0.1) in small populations. Populations with 350 flowering plants or fewer had lost almost all of their rare alleles. While the heterozygosity and inbreeding coefficient were not related to population size, some small populations showed relatively high inbreeding coefficients. In spite of the low genetic differentiation among overall populations (F_ST=0.130), local population structuring was recognized between the two geographically discontinuous population groups. Within groups, sufficient historical gene flow was inferred, whereas a low dispersal ability of this species and geographical separation could produce apparent differentiation between groups.     

Genetic diversity of taro (Colocasia esculenta (L.) Schott) in Vanuatu (Oceania): an appraisal of the distribution of allelic diversity (DAD) with SSR markers

In Vanuatu, an oceanic archipelago located in south-west Pacific, taro (Colocasia esculenta (L.) Schott) is one of the staple crops. An eco-geographical survey of its genetic resources was conducted in ten villages, each located on a different island. A sample of 344 landraces referred as the National Sample (NS) was collected. Its genetic diversity was assessed using nine microsatellites markers and then was compared with an International Core Sample (ICS) that was previously distributed in the ten villages of the study in order to test the geographical distribution of allelic diversity as an effective mean for the on-farm conservation of root crops. The ICS was composed of 41 accessions, including 23 originating from South-East Asia. The molecular dataset revealed in the NS (1) 324 distinct multilocus genotypes, (2) six genetic clusters mainly differentiated by rare alleles, (3) a geographical structure of the genetic resources of taro based, within each village, on the dominance of one or two of these clusters rather that their exclusivity, and (4) an analogy between the patterns of dominant clusters between villages and the past and present social networks. In addition, accessions from the ICS revealed 52 new alleles. Based on these findings, we formulate hypotheses regarding the processes involved in the genetic diversification of taro in Vanuatu. We also discuss the use of this set of microsatellite markers along with the molecular dataset obtained from this study as effective tools to monitor the diversity and evolution of taro in the future.     

First insight into genetic diversity and population structure of the Caucasian wild apple (<Emphasis Type="Italic">Malus orientalis</Emphasis> Uglitzk.) in the Hyrcanian forest (Iran) and its resistance to apple scab and powdery mildew

Investigating population genetic structure and diversity, and resistance to pathogens in crop wild relatives are key steps to assess appropriate conservation and breeding programs. The Caucasian wild apple (Malus orientalis Uglitzk.) is an emblematic fruit tree of the Hyrcanian forest and is supposed to be a contributor to the cultivated apple genome (Malus domestica Borkh. Yet, no study has investigated its population structure, diversity and susceptibility to the two main pathogens of apples, the apple scab (Venturia inaqualis) and the powdery mildew (Podosphaera leucotricha). Here, we investigated population genetic structure and diversity of M. orientalis in the Hyrcanian forest as a mean to identifying future targeted populations for apple conservation and breeding programs. We genotyped using multilocus microsatellite 100 M. orientalis trees sampled in 14 sites. These trees were also screened for presence/absence of six (Rvi6, Vr, Rvi4, Rvi15, Rvi5 and Rvi11) and three (Pl-1, Pl-w, Pl-d) resistance genes to the apple scab and the powdery mildew respectively. Our results showed significant but weak between-site genetic differentiation and isolation by distance pattern suggesting substantial historical gene flow for M. orientalis in this area. We also detected a West-Eastern genetic structure across the Hyrcanian forest with five main populations showing admixture. We also showed a high diversity of resistance genes to apple scab across sites; in contrast, we only found one resistance gene to powdery mildew. These results are a first glimpse to settle wild apple conservation programs in Iran and pinpoint Iranian wild apple populations as an untapped source for apple breeding.